rs7761965

Positions:

• chr6-31305718-G-A
• chr6-31305718-G-T

Variant summary

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

The XR_926691.3(LOC112267902):​n.964+1060C>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 0.135 in 151,184 control chromosomes in the GnomAD database, including 1,694 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 0.14 (1694 hom., cov: 31)
• Consequence: LOC112267902 XR_926691.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.891

Genes affected

LOC112267902 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112267902	XR_926691.3	n.964+1060C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.135 AC: 20450 AN: 151066 Hom.: 1688 Cov.: 31

Gnomad AFR AF: 0.110

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.109

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.135 AC: 20481 AN: 151184 Hom.: 1694 Cov.: 31 AF XY: 0.142 AC XY: 10507 AN XY: 73788

Gnomad4 AFR AF: 0.110

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.358

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.109

Gnomad4 OTH AF: 0.159

Alfa AF: 0.113 Hom.: 1257

Bravo AF: 0.139

Asia WGS AF: 0.320 AC: 1109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7761965; hg19: chr6-31273495;