rs4973768

Variant summary

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

The NM_001321103(SLC4A7):c.*2242G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.44 in 151730 control chromosomes in the gnomAD Genomes database, including 15122 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 0.44 ( 15122 hom., cov: 33)

Consequence

SLC4A7
NM_001321103 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.40

Links

SLC4A7 (HGNC:11033):

(HGNC:):

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.53).

BA1

GnomAd highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC4A7	NM_001321103.2 linkuse as main transcript	c.*2242G>A		3_prime_UTR_variant	26/26	ENST00000454389.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC4A7	ENST00000454389.6 linkuse as main transcript	c.*2242G>A		3_prime_UTR_variant	26/26	1	NM_001321103.2	A1	Q9Y6M7-7
	ENST00000661166.1 linkuse as main transcript	n.975+3980C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.440

AC:

66738

AN:

151730

Hom.:

15122

Cov.:

show subpopulations

Gnomad AFR

AF:

0.358

Gnomad AMI

AF:

0.523

Gnomad AMR

AF:

0.537

Gnomad ASJ

AF:

0.563

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.441

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.583

Gnomad NFE

AF:

0.476

Gnomad OTH

AF:

0.477

GnomAD4 exome

AF:

0.402

AC:

165

AN:

410

Hom.:

AF XY:

0.360

AC XY:

AN XY:

250

show subpopulations

Gnomad4 FIN exome

AF:

0.401

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.250

Alfa

AF:

0.475

Hom.:

40128

Bravo

AF:

0.444

Asia WGS

AF:

0.368

AC:

1276

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.53

Cadd

Benign

Dann

Benign

0.85

Splicing

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

Links

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over