rs320813

Positions:

• chr7-9745624-G-A

Variant summary

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

The ENST00000657272.2(ENSG00000234710):​n.520+2322G>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 0.301 in 151,804 control chromosomes in the GnomAD database, including 7,311 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 0.30 (7311 hom., cov: 33)
• Consequence: ENST00000657272.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.466

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.348 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375148	XR_001745087.3	n.573+2322G>A		intron_variant, non_coding_transcript_variant
LOC105375148	XR_927028.4	n.579+2322G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000657272.2	n.520+2322G>A		intron_variant, non_coding_transcript_variant
	ENST00000447999.1	n.283+2322G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000668655.1	n.495+2322G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45635 AN: 151686 Hom.: 7309 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.438

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.351

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.301 AC: 45646 AN: 151804 Hom.: 7311 Cov.: 33 AF XY: 0.301 AC XY: 22337 AN XY: 74188

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.297

Gnomad4 FIN AF: 0.351

Gnomad4 NFE AF: 0.352

Gnomad4 OTH AF: 0.320

Alfa AF: 0.324 Hom.: 2675

Bravo AF: 0.296

Asia WGS AF: 0.289 AC: 1006 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.0
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs320813; hg19: chr7-9785253;