Variant chr5-6635488-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001047.4(SRD5A1):c.293+1619T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,692 control chromosomes in the GnomAD database, including 20,948 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.52 ( 20948 hom., cov: 33)

Consequence

SRD5A1
NM_001047.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -3.75

Variant links:

Genes affected

SRD5A1 (HGNC:11284): (steroid 5 alpha-reductase 1) Steroid 5-alpha-reductase (EC 1.3.99.5) catalyzes the conversion of testosterone into the more potent androgen, dihydrotestosterone (DHT). Also see SRD5A2 (MIM 607306).[supplied by OMIM, Mar 2008]

SRD5A1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.56 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
SRD5A1	NM_001047.4 linkuse as main transcript	c.293+1619T>C	intron_variant	ENST00000274192.7
SRD5A1	NM_001324322.2 linkuse as main transcript	c.319+1619T>C	intron_variant
SRD5A1	NM_001324323.2 linkuse as main transcript	c.-429+1619T>C	intron_variant
SRD5A1	NR_136739.2 linkuse as main transcript	n.430+1619T>C	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Appris
SRD5A1	ENST00000274192.7 linkuse as main transcript	c.293+1619T>C	intron_variant	1	NM_001047.4	P1
SRD5A1	ENST00000504286.2 linkuse as main transcript	c.293+1619T>C	intron_variant, NMD_transcript_variant	2
SRD5A1	ENST00000510531.6 linkuse as main transcript	c.293+1619T>C	intron_variant, NMD_transcript_variant	2
SRD5A1	ENST00000513117.1 linkuse as main transcript	c.293+1619T>C	intron_variant, NMD_transcript_variant	2

Frequencies

GnomAD3 genomes

AF:

0.523

AC:

79309

AN:

151572

Hom.:

20929

Cov.:

show subpopulations

Gnomad AFR

AF:

0.515

Gnomad AMI

AF:

0.628

Gnomad AMR

AF:

0.570

Gnomad ASJ

AF:

0.534

Gnomad EAS

AF:

0.384

Gnomad SAS

AF:

0.407

Gnomad FIN

AF:

0.552

Gnomad MID

AF:

0.481

Gnomad NFE

AF:

0.530

Gnomad OTH

AF:

0.527

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.523

AC:

79376

AN:

151692

Hom.:

20948

Cov.:

AF XY:

0.521

AC XY:

38589

AN XY:

74114

show subpopulations

Gnomad4 AFR

AF:

0.515

Gnomad4 AMR

AF:

0.570

Gnomad4 ASJ

AF:

0.534

Gnomad4 EAS

AF:

0.384

Gnomad4 SAS

AF:

0.409

Gnomad4 FIN

AF:

0.552

Gnomad4 NFE

AF:

0.530

Gnomad4 OTH

AF:

0.525

Alfa

AF:

0.522

Hom.:

2552

Bravo

AF:

0.529

Asia WGS

AF:

0.440

AC:

1532

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.81

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over