rs6960395

Positions:

• chr7-97193557-G-A

Variant summary

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

The XR_007060445.1(LOC124901704):​n.132-13208C>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 0.708 in 152,032 control chromosomes in the GnomAD database, including 38,364 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 0.71 (38364 hom., cov: 33)
• Consequence: LOC124901704 XR_007060445.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500

Genes affected

LOC124901704 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124901704	XR_007060445.1	n.132-13208C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.708 AC: 107518 AN: 151914 Hom.: 38328 Cov.: 33

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.737

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.731

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.804

Gnomad FIN AF: 0.636

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.708 AC: 107605 AN: 152032 Hom.: 38364 Cov.: 33 AF XY: 0.710 AC XY: 52791 AN XY: 74320

Gnomad4 AFR AF: 0.706

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.731

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.636

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.718

Alfa AF: 0.701 Hom.: 4697

Bravo AF: 0.716

Asia WGS AF: 0.808 AC: 2802 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6960395; hg19: chr7-96822869;