rs611097

Positions:

• chr7-64298295-G-A
• chr7-64298295-G-C
• chr7-64298295-G-T

Variant summary

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

The ENST00000657968.1(ENSG00000287699):​n.219+83C>T 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 0.836 in 152,142 control chromosomes in the GnomAD database, including 55,154 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 0.84 (55154 hom., cov: 32)
• Consequence: ENST00000657968.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.878

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.935 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375322	XR_007060346.1	n.3564+83C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000657968.1	n.219+83C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.836 AC: 127076 AN: 152024 Hom.: 55144 Cov.: 32

Gnomad AFR AF: 0.573

Gnomad AMI AF: 0.940

Gnomad AMR AF: 0.924

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.905

Gnomad SAS AF: 0.888

Gnomad FIN AF: 0.971

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.860

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

GnomAD4 genome AF: 0.836 AC: 127118 AN: 152142 Hom.: 55154 Cov.: 32 AF XY: 0.839 AC XY: 62389 AN XY: 74372

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.924

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.905

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.971

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.861

Alfa AF: 0.881 Hom.: 9517

Bravo AF: 0.821

Asia WGS AF: 0.868 AC: 3017 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs611097; hg19: chr7-63758673;