rs705379

Positions:

• chr7-95324583-G-A
• chr7-95324583-G-C
• chr7-95324583-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.447 in 1,123,462 control chromosomes in the GnomAD database, including 117,043 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.37 (12486 hom., cov: 32)
  • Exomes 𝑓: 0.46 (104557 hom.)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2 O:1
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 7-95324583-G-A is Benign according to our data. Variant chr7-95324583-G-A is described in ClinVar as [Benign]. Clinvar id is 13737.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.476 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.375 AC: 56913 AN: 151920 Hom.: 12490 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.322

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.444

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.435

GnomAD4 exome AF: 0.458 AC: 444754 AN: 971426 Hom.: 104557 Cov.: 13 AF XY: 0.458 AC XY: 227112 AN XY: 496168

Gnomad4 AFR exome AF: 0.126

Gnomad4 AMR exome AF: 0.457

Gnomad4 ASJ exome AF: 0.611

Gnomad4 EAS exome AF: 0.460

Gnomad4 SAS exome AF: 0.401

Gnomad4 FIN exome AF: 0.362

Gnomad4 NFE exome AF: 0.476

Gnomad4 OTH exome AF: 0.455

GnomAD4 genome AF: 0.374 AC: 56917 AN: 152036 Hom.: 12486 Cov.: 32 AF XY: 0.373 AC XY: 27745 AN XY: 74304

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.444

Gnomad4 SAS AF: 0.401

Gnomad4 FIN AF: 0.346

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.435

Alfa AF: 0.408 Hom.: 1946

Bravo AF: 0.376

Asia WGS AF: 0.387 AC: 1348 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	This variant is associated with the following publications: (PMID: 26154629, 11335891, 10669651) -

Enzyme activity finding Other:1

other, no assertion criteria provided

literature only

OMIM

Aug 18, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.9
DANN	Benign	0.91

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs705379; hg19: chr7-94953895; COSMIC: COSV55931894; COSMIC: COSV55931894;