rs1621700

chr6-10419865-C-T

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 0.172 in 152,164 control chromosomes in the GnomAD database, including 3,072 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.17 (3072 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.468

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 6-10419865-C-T is Benign according to our data. Variant chr6-10419865-C-T is described in ClinVar as [Benign]. Clinvar id is 1287998.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.26 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: 0.172 AC: 26136 AN: 152046 Hom.: 3066 Cov.: 33

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.0617

Gnomad SAS AF: 0.196

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.160

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

GnomAD4 genome AF: 0.172 AC: 26157 AN: 152164 Hom.: 3072 Cov.: 33 AF XY: 0.175 AC XY: 13012 AN XY: 74368

Gnomad4 AFR AF: 0.0411

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.0618

Gnomad4 SAS AF: 0.197

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.218

Gnomad4 OTH AF: 0.158

Alfa AF: 0.207 Hom.: 4742

Bravo AF: 0.164

Asia WGS AF: 0.141 AC: 490 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

Jun 28, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	6.1
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1621700; hg19: chr6-10420098;