rs11854994

Variant names:

• chr15-48907195-G-A
• rs11854994
• NM_203349.4:c.657-16384C>T

Variant summary

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

The NM_203349.4(SHC4):​c.657-16384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,372 control chromosomes in the GnomAD database, including 10,985 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 0.35 (10985 hom., cov: 29)
• Consequence: SHC4 NM_203349.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.706
• Publications: 2 publications found

Genes affected

SHC4 (HGNC:16743): (SHC adaptor protein 4) Predicted to enable receptor tyrosine kinase binding activity. Predicted to be involved in transmembrane receptor protein tyrosine kinase signaling pathway. Predicted to act upstream of or within several processes, including apoptotic process; positive regulation of cell population proliferation; and stem cell differentiation. Predicted to be located in postsynaptic membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_203349.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHC4	NM_203349.4	MANE Select	c.657-16384C>T		intron	N/A	NP_976224.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SHC4	ENST00000332408.9	TSL:1 MANE Select	c.657-16384C>T		intron	N/A	ENSP00000329668.4

Frequencies

GnomAD3 genomes AF: 0.353 AC: 53393 AN: 151250 Hom.: 10987 Cov.: 29

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.602

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.323

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.353 AC: 53397 AN: 151372 Hom.: 10985 Cov.: 29 AF XY: 0.347 AC XY: 25660 AN XY: 73932

African (AFR) AF: 0.177 AC: 7328 AN: 41296

American (AMR) AF: 0.376 AC: 5722 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.602 AC: 2087 AN: 3464

East Asian (EAS) AF: 0.120 AC: 620 AN: 5170

South Asian (SAS) AF: 0.433 AC: 2070 AN: 4780

European-Finnish (FIN) AF: 0.323 AC: 3346 AN: 10350

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30645 AN: 67800

Other (OTH) AF: 0.415 AC: 873 AN: 2102

Alfa AF: 0.424 Hom.: 55903

Bravo AF: 0.347

Asia WGS AF: 0.234 AC: 813 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.40
DANN	Benign	0.69
PhyloP100		-0.71
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11854994; hg19: chr15-49199392;