1-247628464-C-T

Position:

• chr1-247628464-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000435333.5(ENSG00000236817):​n.225+7391G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.954 in 152,212 control chromosomes in the GnomAD database, including 69,558 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 0.95 (69558 hom., cov: 31)
• Consequence: ENST00000435333.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.93

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.987 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102724446	XR_426948.4	n.225+7391G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000435333.5	n.225+7391G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000446347.1	n.437+7391G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.955 AC: 145177 AN: 152094 Hom.: 69512 Cov.: 31

Gnomad AFR AF: 0.872

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.974

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.993

Gnomad OTH AF: 0.960

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

GnomAD4 genome AF: 0.954 AC: 145278 AN: 152212 Hom.: 69558 Cov.: 31 AF XY: 0.955 AC XY: 71040 AN XY: 74426

Gnomad4 AFR AF: 0.872

Gnomad4 AMR AF: 0.974

Gnomad4 ASJ AF: 0.948

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.944

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.993

Gnomad4 OTH AF: 0.960

Alfa AF: 0.972 Hom.: 15911

Bravo AF: 0.951

Asia WGS AF: 0.961 AC: 3343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.35
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1306161; hg19: chr1-247791766;