rs1024481

chr7-144410460-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.434 in 151,936 control chromosomes in the GnomAD database, including 15,079 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.43 (15079 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.37

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 7-144410460-G-A is Benign according to our data. Variant chr7-144410460-G-A is described in ClinVar as [Benign]. Clinvar id is 1222264.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.434 AC: 65887 AN: 151818 Hom.: 15073 Cov.: 32

Gnomad AFR AF: 0.425

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.434 AC: 65929 AN: 151936 Hom.: 15079 Cov.: 32 AF XY: 0.440 AC XY: 32675 AN XY: 74244

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.815

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.367

Gnomad4 NFE AF: 0.392

Gnomad4 OTH AF: 0.479

Alfa AF: 0.418 Hom.: 28210

Bravo AF: 0.441

Asia WGS AF: 0.673 AC: 2335 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.12
Dann	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1024481; hg19: chr7-144107553;