rs7703237

Positions:

• chr5-163347720-T-C
• chr5-163347720-T-G

Variant summary

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

The ENST00000646617.1(ENSG00000254186):​n.322+78083A>G 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 0.389 in 151,492 control chromosomes in the GnomAD database, including 12,088 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 0.39 (12088 hom., cov: 30)
• Consequence: ENST00000646617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.46 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377700	XR_001742961.2	n.1236+64599A>G		intron_variant, non_coding_transcript_variant
LOC105377700	XR_001742965.1	n.1236+64599A>G		intron_variant, non_coding_transcript_variant
LOC105377700	XR_002956233.2	n.1236+64599A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000646617.1	n.322+78083A>G		intron_variant, non_coding_transcript_variant
	ENST00000503504.1	n.355+78083A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.389 AC: 58917 AN: 151368 Hom.: 12089 Cov.: 30

Gnomad AFR AF: 0.309

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.0648

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.464

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.389 AC: 58929 AN: 151492 Hom.: 12088 Cov.: 30 AF XY: 0.380 AC XY: 28143 AN XY: 73992

Gnomad4 AFR AF: 0.309

Gnomad4 AMR AF: 0.407

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.0652

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.412

Gnomad4 NFE AF: 0.464

Gnomad4 OTH AF: 0.410

Alfa AF: 0.304 Hom.: 865

Bravo AF: 0.384

Asia WGS AF: 0.195 AC: 681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	11
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7703237; hg19: chr5-162774726;