rs1041856

Variant names:

• chr14-21542814-T-C
• rs1041856

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.367 in 150,890 control chromosomes in the GnomAD database, including 11,159 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 0.37 (11159 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.570
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.458 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.367 AC: 55355 AN: 150774 Hom.: 11162 Cov.: 29

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.0461

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.367 AC: 55366 AN: 150890 Hom.: 11159 Cov.: 29 AF XY: 0.357 AC XY: 26310 AN XY: 73608

African (AFR) AF: 0.283 AC: 11629 AN: 41024

American (AMR) AF: 0.467 AC: 6983 AN: 14946

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1695 AN: 3464

East Asian (EAS) AF: 0.0461 AC: 238 AN: 5168

South Asian (SAS) AF: 0.312 AC: 1495 AN: 4794

European-Finnish (FIN) AF: 0.231 AC: 2385 AN: 10334

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.439 AC: 29793 AN: 67858

Other (OTH) AF: 0.371 AC: 780 AN: 2100

Alfa AF: 0.424 Hom.: 38487

Bravo AF: 0.379

Asia WGS AF: 0.205 AC: 715 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.75
DANN	Benign	0.82
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1041856; hg19: chr14-22010960;